Fiducials for use in registration of a patterned surface

Abstract

Registration of a patterned flow cell may utilize fiducials comprising sets or groupings of features (e.g., sites, sample wells, nanowells) having known locations and in which the placement of the features is not in accordance with a periodic pattern or is otherwise distinguishable from the periodic pattern of sites present in non-fiducial regions of the flow cell substrate. In certain embodiments the positioning of the sites that are part of the fiducial represent a break or discontinuity in the periodic pattern of sites that are otherwise present on the surface of a patterned flow cell.

1 . A patterned flow cell, comprising:
 a substrate;   a first plurality of sample sites formed on the substrate, wherein the first plurality of sample sites are arranged in a periodic pattern; and   a second plurality of sample sites formed on the substrate, wherein the second plurality of sample sites are arranged in a non-period arrangement, wherein the second plurality of sample sites are fiducials.   
     
     
         2 . The patterned flow cell of  claim 1 , wherein the sample sites of the first plurality and second plurality of sample sites comprise sample wells configured to bind biopolymers for processing. 
     
     
         3 . The patterned flow cell of  claim 1 , wherein the periodic pattern comprises a hexagonal pattern or a rectilinear pattern. 
     
     
         4 . The patterned flow cell of  claim 1 , wherein the non-periodic arrangement comprises a random or statistically pseudorandom arrangement of the second plurality of sample sites. 
     
     
         5 . The patterned flow cell of  claim 1 , wherein the second plurality of sample sites corresponds to a break in the periodic pattern in which the first plurality of sample sites are arranged. 
     
     
         6 . The patterned flow of  claim 1 , wherein the non-periodic arrangement of sample sites for each fiducial comprises a different respective non-periodic arrangement relative to other fiducials. 
     
     
         7 . The patterned flow of  claim 1 , wherein at least two fiducials have the same non-periodic arrangement of sample sites. 
     
     
         8 . The patterned flow cell of  claim 1 , each fiducial has an area of between 8×8 pixels to 1024×1024 pixels within an image tile acquired of the patterned flow cell. 
     
     
         9 . The patterned flow cell of  claim 1 , wherein each respective set of sample sites corresponding to a respective fiducial comprises between 20 to 50 sample sites at a lower bound and up to 500,000 sample sites at an upper bound. 
     
     
         10 . The patterned flow cell of  claim 1 , wherein each fiducial further comprises a ring or arcuate structure, wherein each ring or arcuate structure comprises an additional set of sample sites arranged to form the ring or arcuate structure. 
     
     
         11 . A method for registering an image acquired of a patterned flow cell, the method comprising:
 acquiring an image of a patterned flow cell comprising a plurality of sample sites in a periodic pattern and a plurality of fiducials, each fiducial comprising sample sites in a respective non-periodic arrangement;   comparing image data corresponding to each fiducial to one or more respective templates comprising known location data for the respective non-periodic arrangement of sample sites for each fiducial;   deriving one or more geometric transforms based on the comparison of the image data to the one or more templates; and   transforming the plurality of sample sites of the patterned flow cell using the one or more geometric transforms.   
     
     
         12 . The method of  claim 11 , further comprising:
 generating the one or more respective templates from design data comprising the known locations of at least the sample site in the respective non-periodic arrangements forming the fiducials.   
     
     
         13 . The method of  claim 11 , wherein the step of comparing image data corresponding to each fiducial to one or more respective templates comprises performing a cross-correlation and generating a set of x-, y-offsets as an output of the cross-correlation. 
     
     
         14 . The method of  claim 13 , wherein the one or more geometric transforms are derived using the x-, y-offsets. 
     
     
         15 . The method of  claim 11 , wherein each fiducial further comprises a ring or arcuate structure comprising a plurality of additional sample sites, wherein the one or more respective templates further comprise known location data for the plurality of additional sample sites forming the ring or arcuate structures. 
     
     
         16 . The method of  claim 15 , further comprising:
 performing an initial comparison of the image data corresponding to the ring or arcuate structures of each fiducial to the one or more respective templates;   deriving an initial geometric transform based on the initial comparison; and   using the initial geometric transform as part of the step of comparing the image data corresponding to each fiducial to the one or more respective templates comprising known location data for the respective non-periodic arrangement of sample sites for each fiducial.   
     
     
         17 . A patterned flow cell, comprising:
 a substrate;   a plurality of sample sites formed on the substrate, wherein the plurality of sites are arranged non-periodically over the substrate.   
     
     
         18 . The patterned flow cell of  claim 17 , wherein the patterned flow cell does not comprise separate and distinct fiducials within the plurality of sample sites. 
     
     
         19 . The patterned flow cell of  claim 17 , wherein the plurality of sample sites comprise sample wells configured to bind biopolymers for processing. 
     
     
         20 . The patterned flow cell of  claim 17 , wherein the plurality of sample sites are arranged in a random or statistically pseudorandom arrangement. 
     
     
         21 . A patterned flow cell, comprising:
 a substrate;   a first plurality of sample sites formed on the substrate, wherein the first plurality of sample sites are arranged in a first periodic pattern; and   a second plurality of sample sites formed on the substrate, wherein the second plurality of sample sites are arranged in a second periodic pattern different from the first periodic pattern, wherein the difference between the first periodic pattern and the second periodic pattern allow the some or all of the first plurality of sample sites or the second plurality of sample sites to serve as a fiducial.   
     
     
         22 . The patterned flow cell of  claim 21 , wherein the difference between the first periodic pattern and the second periodic pattern comprises one or more of a difference in pitch, pattern type, shape or geometry of the respective sample sites, offset, or rotation. 
     
     
         23 . The patterned flow cell of  claim 21 , wherein the sample sites of the first plurality and second plurality of sample sites comprise sample wells configured to bind biopolymers for processing. 
     
     
         24 . The patterned flow cell of  claim 21 , wherein the one or both of the first periodic pattern or the second periodic pattern comprises a hexagonal pattern or a rectilinear pattern. 
     
     
         25 . The patterned flow cell of  claim 21 , wherein the difference between the first periodic pattern and the second periodic pattern corresponds to a break in one or both patterns that is indicative of a fiducial.